Merge 7bd8edf into da5a3ce

.github/workflows/ci.yml

@@ -87,14 +87,17 @@ jobs:
         with:
           parallel: true
           flag-name: Unit Test
-      - name: run Codacy coverage reporter
-        uses: codacy/codacy-coverage-reporter-action@master
-        with:
-          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          coverage-reports: coverage.xml
-        env:
-          secrets.CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
-        if: "${{ (matrix.python-version == '3.8') && (matrix.postgres-version == '12') && (!!env.CODACY_PROJECT_TOKEN) }}"
+      - name: Check import order with isort
+        run: |
+          rm -rf src
+          isort --force-sort-within-sections --profile=black --check .
+        if: ${{ matrix.python-version == '3.8' }}
+      - name: Check style with black
+        run: black --check --line-length 100 .
+        if: ${{ matrix.python-version == '3.8' }}
+      - name: Run linting
+        run: flake8
+        if: ${{ matrix.python-version == '3.8' }}
 
   coveralls_finish:
     needs: build

Makefile

@@ -62,3 +62,18 @@ test: collectstatic
 .PHONY: test-noselenium
 test-noselenium:
 	VARFISH_KIOSK_MODE=0 SKIP_SELENIUM=1 coverage run manage.py test -v2 --settings=config.settings.test
+
+.PHONY: lint
+lint: flake8
+
+.PHONY: isort
+isort:
+	isort --force-sort-within-sections --profile=black .
+
+.PHONY: flake8
+flake8:
+	flake8
+
+coverage:
+	coverage report
+	coverage html

README.rst

@@ -1,10 +1,6 @@
 .. image:: https://readthedocs.org/projects/varfish-server/badge/?version=latest
     :target: https://varfish-server.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
-.. image:: https://app.codacy.com/project/badge/Grade/f47216cf5a4349acbb9baf5ca1c91329
-    :target: https://www.codacy.com/gh/bihealth/varfish-server/dashboard?utm_source=github.com&utm_medium=referral&utm_content=bihealth/varfish-server&utm_campaign=Badge_Grade
-.. image:: https://app.codacy.com/project/badge/Coverage/f47216cf5a4349acbb9baf5ca1c91329
-    :target: https://www.codacy.com/gh/bihealth/varfish-server/dashboard?utm_source=github.com&utm_medium=referral&utm_content=bihealth/varfish-server&utm_campaign=Badge_Coverage
 .. image:: https://coveralls.io/repos/github/bihealth/varfish-server/badge.svg?branch=main
     :target: https://coveralls.io/github/bihealth/varfish-server?branch=main
 .. image:: https://img.shields.io/badge/License-MIT-green.svg

beaconsite/forms.py

@@ -2,7 +2,7 @@
 from django.db import transaction
 from projectroles.models import Project
 
-from .models import Consortium, Site, ConsortiumMember, ConsortiumAssignment
+from .models import Consortium, ConsortiumAssignment, ConsortiumMember, Site
 
 
 class ConsortiumForm(forms.ModelForm):

beaconsite/migrations/0001_initial.py

@@ -2,11 +2,12 @@
 # Generated by Django 1.11.29 on 2021-03-03 08:23
 from __future__ import unicode_literals
 
+import uuid
+
+import cryptographic_fields.fields
 from django.conf import settings
 from django.db import migrations, models
 import django.db.models.deletion
-import cryptographic_fields.fields
-import uuid
 
 
 class Migration(migrations.Migration):

beaconsite/migrations/0003_auto_20210304_1052.py

@@ -2,8 +2,8 @@
 # Generated by Django 1.11.29 on 2021-03-04 10:52
 from __future__ import unicode_literals
 
-from django.db import migrations
 import cryptographic_fields.fields
+from django.db import migrations
 
 
 class Migration(migrations.Migration):

beaconsite/models.py

@@ -2,12 +2,12 @@
 import uuid as uuid_object
 
 from Crypto.PublicKey import RSA
+from cryptographic_fields.fields import EncryptedTextField
+from django.conf import settings
 from django.core.exceptions import ValidationError
 from django.db import models
-from django.conf import settings
 from django.urls import reverse
 from projectroles.models import Project
-from cryptographic_fields.fields import EncryptedTextField
 
 #: Django user model.
 AUTH_USER_MODEL = getattr(settings, "AUTH_USER_MODEL", "auth.User")

beaconsite/models_api.py

@@ -2,7 +2,6 @@
 
 import attr
 
-
 #: Default assembly ID to assume.
 DEFAULT_ASSEMBLY_ID = "GRCh37"
 #: Indicated API version.

beaconsite/plugins.py

@@ -1,4 +1,3 @@
-from bgjobs.plugins import BackgroundJobsPluginPoint
 from projectroles.plugins import SiteAppPluginPoint
 
 from .urls import urlpatterns

beaconsite/rules.py

@@ -1,8 +1,6 @@
 """Rule definitions for the ``beaconsites`` app."""
 
 import rules
-from projectroles import rules as pr_rules
-
 
 # Rules ------------------------------------------------------------------------
 

beaconsite/tests/factories.py

@@ -3,8 +3,9 @@
 from projectroles.models import Project
 
 from varfish.users.tests.factories import UserFactory
-from variants.tests.factories import ProjectFactory, CaseFactory
-from ..models import Site, Consortium, ConsortiumMember, Query, Response, ConsortiumAssignment
+from variants.tests.factories import CaseFactory, ProjectFactory
+
+from ..models import Consortium, ConsortiumAssignment, ConsortiumMember, Query, Response, Site
 
 
 class SiteFactory(factory.django.DjangoModelFactory):

beaconsite/tests/test_models.py

@@ -2,15 +2,15 @@
 from django.core.exceptions import ValidationError
 from test_plus.test import TestCase
 
+from ..models import Consortium, ConsortiumMember, Query, Response, Site
 from .factories import (
-    SiteFactory,
     ConsortiumFactory,
     ConsortiumMemberFactory,
     ConsortiumWithLocalAndRemoteSiteFactory,
     QueryFactory,
     ResponseFactory,
+    SiteFactory,
 )
-from ..models import Site, Consortium, ConsortiumMember, Query, Response
 
 
 class TestSite(TestCase):

beaconsite/tests/test_permissions_ajax.py

@@ -2,21 +2,23 @@
 
 import cattr
 from django.urls import reverse
-
 from projectroles.tests.test_permissions_api import TestProjectAPIPermissionBase
 import requests_mock
 
-from .factories import SiteFactory
 from ..models import Site
 from ..models_api import BeaconAlleleRequest
+from .factories import SiteFactory
 
 
 class TestOrganisationAjaxViews(TestProjectAPIPermissionBase):
     @requests_mock.Mocker()
     def test_get(self, r_mock):
         _local_site = SiteFactory(role=Site.LOCAL)
         remote_site = SiteFactory()
-        url = reverse("beaconsite:ajax-beacon-info", kwargs={"site": remote_site.sodar_uuid},)
+        url = reverse(
+            "beaconsite:ajax-beacon-info",
+            kwargs={"site": remote_site.sodar_uuid},
+        )
         good_users = [
             self.superuser,
         ]
@@ -71,7 +73,10 @@ def test_get(self, r_mock):
         url_params = "&".join(
             "%s=%s" % (k, v) for k, v in cattr.unstructure(beacon_allele_request).items()
         )
-        url = reverse("beaconsite:ajax-beacon-query", kwargs={"site": remote_site.sodar_uuid},)
+        url = reverse(
+            "beaconsite:ajax-beacon-query",
+            kwargs={"site": remote_site.sodar_uuid},
+        )
         good_users = [
             self.superuser,
         ]

beaconsite/tests/test_permissions_api.py

@@ -1,20 +1,21 @@
-import urllib
 import datetime
+import urllib
 from wsgiref.handlers import format_date_time
 
-import cattr
-import httpsig
 from Crypto.PublicKey import RSA
+import cattr
 from django.shortcuts import reverse
 from django.utils import timezone
+import httpsig
 from projectroles.tests.test_permissions_api import TestProjectAPIPermissionBase
 from requests_http_signature import HTTPSignatureAuth
 
 from variants.tests.factories import SmallVariantFactory
+
 from ..models import Site
-from .factories import ConsortiumWithLocalAndRemoteSiteFactory, ConsortiumAssignmentFactory
 from ..models_api import BeaconAlleleRequest
 from ..views_api import _header_canonical
+from .factories import ConsortiumAssignmentFactory, ConsortiumWithLocalAndRemoteSiteFactory
 
 
 class AcceptHeaderMixin:
@@ -48,7 +49,8 @@ def setUp(self):
         self.consortium = ConsortiumWithLocalAndRemoteSiteFactory()
         self.remote_site = Site.objects.get(role=Site.REMOTE)
         ConsortiumAssignmentFactory(
-            consortium=self.consortium, project=self.project,
+            consortium=self.consortium,
+            project=self.project,
         )
 
     def test_success(self):
@@ -115,7 +117,8 @@ def setUp(self):
         self.consortium = ConsortiumWithLocalAndRemoteSiteFactory()
         self.remote_site = Site.objects.get(role=Site.REMOTE)
         ConsortiumAssignmentFactory(
-            consortium=self.consortium, project=self.project,
+            consortium=self.consortium,
+            project=self.project,
         )
         self.small_variant = SmallVariantFactory(case__project=self.project)
         self.beacon_allele_request = BeaconAlleleRequest(

beaconsite/tests/test_views.py

@@ -187,7 +187,10 @@ class TestSiteUpdateView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(
-                reverse("beaconsite:site-update", kwargs={"site": self.site.sodar_uuid},)
+                reverse(
+                    "beaconsite:site-update",
+                    kwargs={"site": self.site.sodar_uuid},
+                )
             )
         self.assertEqual(response.status_code, 200)
         self.assertIsNotNone(response.context["object"])
@@ -211,7 +214,10 @@ def test_update(self):
 
         with self.login(self.superuser):
             response = self.client.post(
-                reverse("beaconsite:site-update", kwargs={"site": self.site.sodar_uuid},),
+                reverse(
+                    "beaconsite:site-update",
+                    kwargs={"site": self.site.sodar_uuid},
+                ),
                 post_data,
             )
 
@@ -243,7 +249,10 @@ class TestSiteDeleteView(TestViewsBase):
     def test_render(self):
         with self.login(self.superuser):
             response = self.client.get(
-                reverse("beaconsite:site-delete", kwargs={"site": self.site.sodar_uuid},)
+                reverse(
+                    "beaconsite:site-delete",
+                    kwargs={"site": self.site.sodar_uuid},
+                )
             )
             self.assertEqual(response.status_code, 200)
 
@@ -253,7 +262,10 @@ def test_delete(self):
 
         with self.login(self.superuser):
             response = self.client.post(
-                reverse("beaconsite:site-delete", kwargs={"site": self.site.sodar_uuid},)
+                reverse(
+                    "beaconsite:site-delete",
+                    kwargs={"site": self.site.sodar_uuid},
+                )
             )
             self.assertEqual(response.status_code, 302)
             self.assertEqual(response.url, reverse("beaconsite:site-list"))

beaconsite/tests/test_views_ajax.py

@@ -5,7 +5,6 @@
 from projectroles.tests.test_permissions_api import TestProjectAPIPermissionBase
 import requests_mock
 
-
 RE_UUID4 = re.compile(r"^[0-9a-f-]+$")
 RE_DATETIME = re.compile(r"^\d\d\d\d-\d\d-\d\dT\d\d:\d\d:\d\d\.\d\d\d\d\d\dZ$")
 

beaconsite/tests/test_views_api.py

@@ -3,10 +3,11 @@
 
 from variants.tests.factories import SmallVariantFactory
 from variants.tests.helpers import ApiViewTestBase
-from .test_permissions_api import AcceptHeaderMixin
+
 from ..models import Site
-from .factories import ConsortiumWithLocalAndRemoteSiteFactory, ConsortiumAssignmentFactory
 from ..models_api import BeaconAlleleRequest
+from .factories import ConsortiumAssignmentFactory, ConsortiumWithLocalAndRemoteSiteFactory
+from .test_permissions_api import AcceptHeaderMixin
 
 
 class TestBeaconInfoApiView(AcceptHeaderMixin, ApiViewTestBase):
@@ -16,7 +17,8 @@ def setUp(self):
         self.local_site = Site.objects.get(role=Site.LOCAL)
         self.remote_site = Site.objects.get(role=Site.REMOTE)
         ConsortiumAssignmentFactory(
-            consortium=self.consortium, project=self.project,
+            consortium=self.consortium,
+            project=self.project,
         )
 
     def test_get_info(self):
@@ -54,7 +56,8 @@ def setUp(self):
         self.local_site = Site.objects.get(role=Site.LOCAL)
         self.remote_site = Site.objects.get(role=Site.REMOTE)
         ConsortiumAssignmentFactory(
-            consortium=self.consortium, project=self.project,
+            consortium=self.consortium,
+            project=self.project,
         )
         self.small_variant = SmallVariantFactory(case__project=self.project)
         self.beacon_allele_request = BeaconAlleleRequest(

beaconsite/urls.py

@@ -2,13 +2,22 @@
 """
 
 from django.conf.urls import url
-from . import views, views_api, views_ajax
+
+from . import views, views_ajax, views_api
 
 app_name = "beaconsite"
 
 ui_urlpatterns = [
-    url(regex=r"^$", view=views.IndexView.as_view(), name="index",),
-    url(regex=r"^consortium$", view=views.ConsortiumListView.as_view(), name="consortium-list",),
+    url(
+        regex=r"^$",
+        view=views.IndexView.as_view(),
+        name="index",
+    ),
+    url(
+        regex=r"^consortium$",
+        view=views.ConsortiumListView.as_view(),
+        name="consortium-list",
+    ),
     url(
         regex=r"^consortium/(?P<consortium>[0-9a-f-]+)$",
         view=views.ConsortiumDetailView.as_view(),
@@ -29,13 +38,21 @@
         view=views.ConsortiumDeleteView.as_view(),
         name="consortium-delete",
     ),
-    url(regex=r"^site$", view=views.SiteListView.as_view(), name="site-list",),
+    url(
+        regex=r"^site$",
+        view=views.SiteListView.as_view(),
+        name="site-list",
+    ),
     url(
         regex=r"^site/(?P<site>[0-9a-f-]+)$",
         view=views.SiteDetailView.as_view(),
         name="site-detail",
     ),
-    url(regex=r"^site/create/$", view=views.SiteCreateView.as_view(), name="site-create",),
+    url(
+        regex=r"^site/create/$",
+        view=views.SiteCreateView.as_view(),
+        name="site-create",
+    ),
     url(
         regex=r"^site/update/(?P<site>[0-9a-f-]+)$",
         view=views.SiteUpdateView.as_view(),